(248j) Dynamic Strategies for Target-Site Localization by Gene Regulatory Proteins

Gene expression is orchestrated by a host of regulatory proteins that coordinate the transcription of DNA to RNA. Regulatory proteins function by locating specific binding sequences of DNA and binding to these sequences to form the transcription initiation complex. In many instances, these regulatory proteins only have several hundred copies that must efficiently locate target sequences on the genome-length DNA strand. The non-specific binding of regulatory proteins to random sequences of DNA is believed to permit the protein to slide along the DNA in a stochastic manner. Periodically, a thermal kick or an interaction with another bound protein will disengage the regulatory protein from the DNA surface, leading to three-dimensional diffusion. Eventually, the protein will reattach to the DNA at some new location that is dictated by both the diffusivity of the protein and the DNA configuration. Cycling through these random events constitutes a search strategy for the target site. We build a reaction-diffusion theory of this search process in order to predict the optimal strategy for target site localization. The statistical behavior of the DNA strand acts as a necessary input into the theory, and we consider several governing behaviors for the DNA strand. We explore the impact of DNA configuration on target site localization in order to predict how protein expression will vary under different experimental conditions.